Re: [AMBER] Generalized Born and entropy

From: David Case <>
Date: Wed, 8 Jan 2020 15:30:25 +0000

On Wed, Jan 08, 2020, Martin Rosellen wrote:
>My question is if there is a part in the
>script that approximates the entropy of hydrophobic interactions?

No. Just like there is nothing that tries to figure out the entropy of
electrostatic interactions. GB numbers are estimates of free energies only.

Note 1: the configurational entropy calculation is a completely
different beast, and has nothing to do with implicit solvation models.

Note 2: the 3D-RSIM implicit solvent model does provide estimates of
enthalpy and entropy (as well as free energy) for all interaction types.
I would characterize the results for test cases we have made a "OK but
not great". To draw your own conclusions, see:

J. Johnson, D.A. Case, T. Yamazaki, S. Gusarov, A. Kovalenko
and T. Luchko. Small Molecule Solvation Energy and Entropy from
3D-RISM. J. Phys. Cond. Mat. 28, 344002 (2016).


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Received on Wed Jan 08 2020 - 08:00:02 PST
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